We don't recommend installing the Intel® Optane™ SSD 900P Series on the PCIe 3.0 x16 (x2 mode). As you suggested, even though it fits a x16 device, it'll have have the bandwidth of a x2 one.

Regarding the positioning of the cards, it's recommended to install the video card on the PCIe 3.0 x16 closest to the CPU and the Intel® Optane™ SSD 900P Series on the other available PCIe 3.0 x16. The drive has been tested with some mATX motherboards, so it should be alright as long as there's airflow across the cards to provide cooling.

We recommend connecting the SSD to CPU PCIe lanes when possible as they tend to have better performance. However, if you want to distance the cards a PCIe 3.0 x16 (x4 mode) should work fine. We recommend checking with your system/motherboard manufacturer just to make sure that PCIe slot doesn't share bandwidth with other slots on the board.

Which PCIe slots are linked to the CPU and which ones are to the Chipset is defined by the motherboard manufacturer and varies from model to model. It is recommended to check the motherboard's manual in order to be sure.

As per your other question, the Intel® Optane™ SSD 900P Series is not available in M.2 form factor, though it's available in 1/2 Height (Add-In-Card) and 2.5" (with an U.2 to M.2 cable adapter). As with other models that offer both Add-In-Card and M.2, it'll come to your personal preference and available space and slots to decide which to use.